Contacts of the helix formed by residues 99 - 111 (chain B) in PDB entry 3DCG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO* 3.5 32.1 - - + -
68B HIS* 3.9 27.8 - - + +
69B VAL* 4.9 2.4 - - + +
72B LYS* 3.6 33.9 - - + -
95B ILE* 3.8 11.0 - - + -
96B ALA* 3.0 29.0 + - + +
98B GLU* 1.3 75.5 - - - +
100B ALA* 1.3 60.0 + - - +
101B LEU 3.4 2.4 + - - -
102B GLU* 3.4 12.8 + - - +
103B LEU* 2.9 43.4 + - + +
50C LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.1 5.6 - - + -
96B ALA 3.4 5.8 + - - +
97B PRO* 3.4 16.5 + - + +
98B GLU 3.5 0.2 - - - -
99B ILE* 1.3 78.1 - - - +
101B LEU* 1.3 56.8 + - - +
103B LEU* 3.3 7.7 + - - +
104B LEU* 2.8 30.2 + - - +
149F ALA* 3.4 26.4 - - - +
152F ALA* 4.0 16.8 - - + -
153F LEU* 3.7 12.3 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PRO 4.7 0.6 + - - -
98B GLU 5.4 0.4 + - - -
99B ILE 3.4 0.4 - - - -
100B ALA* 1.3 75.4 - - - +
102B GLU* 1.3 60.8 + - + +
104B LEU* 3.3 17.7 + - + +
105B MET* 3.0 46.7 + - + +
153F LEU* 4.0 29.7 - - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.4 26.9 - - + +
66B PRO* 4.1 13.4 - - + +
68B HIS* 2.8 35.7 + - - -
69B VAL* 3.7 14.1 - - + +
98B GLU 5.7 0.4 - - - +
99B ILE* 3.4 11.0 + - - +
101B LEU* 1.3 79.9 - - + +
103B LEU* 1.3 57.6 + - - +
105B MET* 3.5 12.2 + - - +
106B ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.9 17.2 - - + +
72B LYS* 4.2 9.9 - - + -
73B VAL* 3.8 18.8 - - + -
93B PHE* 4.9 0.4 - - + -
95B ILE* 3.8 42.8 - - + -
99B ILE* 2.9 32.3 + - + +
100B ALA* 3.4 6.5 - - - +
102B GLU* 1.3 74.9 - - - +
104B LEU* 1.3 54.9 + - - +
106B ALA 3.4 0.2 + - - -
107B ALA* 2.8 37.4 + - - +
145F LEU* 3.8 32.1 - - + -
149F ALA* 4.2 7.0 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA 2.8 14.1 + - - +
101B LEU* 3.3 27.4 - - + +
103B LEU* 1.3 73.0 - - - +
105B MET* 1.3 61.4 + - + +
107B ALA* 3.8 2.9 - - - +
108B ASN* 2.9 31.6 + - + +
146F GLN* 3.9 35.4 - - + +
149F ALA* 3.7 11.4 - - + +
150F LEU* 4.5 18.6 - - + +
153F LEU* 4.6 10.1 - - + -
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 3.0 31.7 + - + +
102B GLU* 3.6 12.8 - - - +
104B LEU* 1.3 81.3 - - + +
106B ALA* 1.3 56.9 + - - +
108B ASN* 3.4 6.7 + - - +
109B PHE* 3.0 29.2 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.0 27.1 - - + -
69B VAL* 3.6 23.3 - - + -
73B VAL* 4.5 7.4 - - + -
102B GLU 3.0 18.3 + - - +
103B LEU 3.6 2.9 - - - +
105B MET* 1.3 75.9 - - - +
107B ALA* 1.3 51.9 + - - +
109B PHE* 3.2 6.6 + - - +
110B LEU* 2.8 40.1 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 5.6 0.2 - - - -
103B LEU 2.8 21.0 + - - +
104B LEU 3.8 0.9 - - - +
106B ALA* 1.3 68.4 - - - +
108B ASN* 1.3 60.2 + - - +
110B LEU* 3.5 1.7 - - - -
111B ASP 2.8 24.6 + - - -
112B CYS* 3.2 21.7 + - - +
145F LEU* 3.8 35.8 - - + +
146F GLN* 3.4 22.8 + - + +
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 2.9 22.5 + - + +
105B MET* 3.5 7.5 + - - +
107B ALA* 1.3 75.5 - - - +
109B PHE* 1.3 68.1 + - - +
111B ASP* 3.1 14.0 + - - +
146F GLN* 3.6 26.2 + - - +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 2.7 38.5 + - + +
45B MET* 5.2 6.3 - - + -
62B PHE* 4.1 26.7 - + - -
64B GLU* 4.2 26.7 - - + -
65B ILE* 4.3 10.1 - - + -
105B MET 3.0 14.6 + - - +
106B ALA* 3.2 8.7 + - - +
108B ASN* 1.3 81.8 - - - +
110B LEU* 1.3 63.4 + - + +
111B ASP* 4.7 0.2 - - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 2.7 35.3 + - - +
40B GLY 3.4 0.3 + - - -
41B THR* 3.4 13.3 + - + -
42B ILE* 4.2 7.4 - - + -
62B PHE* 3.6 36.3 - - + -
65B ILE* 4.1 17.5 - - + -
70B LEU* 5.2 3.4 - - + -
73B VAL* 3.6 37.2 - - + -
77B PHE* 4.9 3.6 - - + -
106B ALA 2.8 22.9 + - - +
107B ALA 3.3 3.3 + - - +
108B ASN 3.2 0.2 - - - -
109B PHE* 1.3 77.5 - - + +
111B ASP* 1.3 71.4 + - - +
112B CYS* 4.1 9.9 - - - -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR 4.0 2.8 - - - +
40B GLY* 3.3 23.4 + - - -
41B THR* 3.8 14.6 - - - +
107B ALA 2.8 9.6 + - - -
108B ASN 3.1 11.0 + - - +
110B LEU* 1.3 81.9 - - - +
112B CYS* 1.3 56.0 + - - +
146F GLN* 4.3 8.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il